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1 Galaxy tool to back-translate a protein alignment to nucleotides
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2 ================================================================
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3
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4 This tool is copyright 2012-2014 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below (MIT licence).
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7
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8 This tool is a short Python script (using Biopython library functions) to
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9 load a protein alignment, and matching nucleotide FASTA file of unaligned
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10 sequences, which are threaded onto the protein alignment in order to produce
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11 a codon aware nucleotide alignment - which can be viewed as a back translation.
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12
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13 This tool is available from the Galaxy Tool Shed at:
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14
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15 * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
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16
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1
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17 The underlying Python script can also be used outside of Galaxy, for
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18 details run::
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19
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20 $ python align_back_trans.py
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0
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21
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22 Automated Installation
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23 ======================
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24
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25 This should be straightforward using the Galaxy Tool Shed, which should be
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26 able to automatically install the dependency on Biopython, and then install
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27 this tool and run its unit tests.
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28
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29
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30 Manual Installation
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31 ===================
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32
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33 There are just two files to install to use this tool from within Galaxy:
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34
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35 * ``align_back_trans.py`` (the Python script)
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36 * ``align_back_trans.xml`` (the Galaxy tool definition)
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37
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38 The suggested location is in a dedicated ``tools/align_back_trans`` folder.
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39
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40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
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41 the tool. One suggested location is in the multiple alignments section. Simply
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42 add the line::
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43
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44 <tool file="align_back_trans/align_back_trans.xml" />
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45
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46 You will also need to install Biopython 1.62 or later. If you want to run
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47 the unit tests, include this line in ``tools_conf.xml.sample`` and the sample
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48 FASTA files under the ``test-data`` directory. Then::
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49
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50 ./run_functional_tests.sh -id align_back_trans
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51
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52 That's it.
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53
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54
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55 History
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56 =======
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57
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58 ======= ======================================================================
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59 Version Changes
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60 ------- ----------------------------------------------------------------------
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61 v0.0.1 - Initial version, based on a previously written Python script
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62 v0.0.2 - Optionally check the translation is consistent
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63 v0.0.3 - First official release
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64 v0.0.4 - Simplified XML to apply input format to output data.
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65 - Fixed error message when sequence length not a multiple of three.
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66 ======= ======================================================================
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67
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68
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69 Developers
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70 ==========
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71
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72 This script was initially developed on this repository:
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73 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
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74
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75 With the addition of a Galaxy wrapper, developement moved here:
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76 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
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77
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78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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79 the following command from the Galaxy root folder::
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80
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81 $ tar -czf align_back_trans.tar.gz tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml test-data/demo_nucs.fasta test-data/demo_nucs_trailing_stop.fasta test-data/demo_prot_align.fasta test-data/demo_nuc_align.fasta
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82
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83 Check this worked::
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84
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85 $ tar -tzf align_back_trans.tar.gz
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86 tools/align_back_trans/README.rst
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87 tools/align_back_trans/align_back_trans.py
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88 tools/align_back_trans/align_back_trans.xml
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89 tools/align_back_trans/tool_dependencies.xml
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90 test-data/demo_nucs.fasta
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91 test-data/demo_nucs_trailing_stop.fasta
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92 test-data/demo_prot_align.fasta
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93 test-data/demo_nuc_align.fasta
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94
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95
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96 Licence (MIT)
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97 =============
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98
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99 Permission is hereby granted, free of charge, to any person obtaining a copy
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100 of this software and associated documentation files (the "Software"), to deal
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101 in the Software without restriction, including without limitation the rights
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102 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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103 copies of the Software, and to permit persons to whom the Software is
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104 furnished to do so, subject to the following conditions:
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105
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106 The above copyright notice and this permission notice shall be included in
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107 all copies or substantial portions of the Software.
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108
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109 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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110 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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111 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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112 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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113 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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114 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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115 THE SOFTWARE.
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